The Doctor's Daughter
by Articuno54
Summary: Harry and Hermione have been forced to run from the Ministry. On the run, the two are teared apart and turned against each other. The Doctor drops in for a surprise visit. Will The Doctor be able to save his own daughter from the corrupt Ministry, or will she be the end of him? -My first attempt at a Crossover and Doctor Who fic.
1. Chapter 1

Voldemort had fallen, but the Ministry was as corrupt as ever. Harry and Hermione were still running, 2 months after the defeat of Voldemort. The Ministry needed at new person for the wizard population, and they had chosen him. They had counted up any crimes that he committed while killing their Dark Lord for them, and began to hunt him. He didn't know how severe his punishment would be, but he did not intend to find out. He didn't mean do drag Hermione into this but she was the main reason he got away, making her an accomplice to the crime. They had been doing fine, but eventually their luck had to run out though…

"_Bombarda Maxima!" _

_A loud explosion rang out close by._

"_We got to go!" Yelled Harry as he quickly gathered what little items they had._

"_I know Harry, where do we go now?"_

"_Maybe America, big place from what I've heard."_

"_Whatever you say, I'll follow you."_

_The two sprinted out of the tent, trying to get as far away from the Ministry as possible._

"_Stupefy!" "Sectumsempra!" _

_Hermione was blasted into a tree while Harry began to bleed profusely, writhing on the ground in pain. Suddenly, a black blur appeared a disposed of all the wizards._

_Hermione ran towards Harry, trying to heal the wounds._

"_There's only one way to keep him alive now. You look like a smart girl, you know what I have to do right?"_

_The man was pale skinned with blood red, slit eyes. His hair was stark white and wore a black cloak that covered all of his form. He also had a long rapier strapped to his side._

"_Who are you and how do you know me?"_

"_I'm Damien Nightingale, I've been watching you in my forest. I can help, but only if you want me to."_

"_You seem trustworthy, and I don't have much of a choice. Make sure he lives; I'm going to lead the others away. No doubt they called in reinforcements. They'll kill you on sight but they'll capture me, giving you more time." She lightly kissed Harry on the forehead. "See you later, love."_

_Hermione dashed in the opposite direction, casting one more look at Harry after he whispered her name, he was begging her not to leave him. She ran for 60 seconds before loudly yelling, "Come on Harry, we need to keep moving!" at the top of her lungs._

_Damien took Harry's bleeding form and raced back to his hidden hut. He closed the wounds and then, he bit him._

That was his last significant memory, when Hermione left him over a year ago. Only two things could have happened to her, she is either dead or has been taken by the Ministry. He didn't like either of those options but if she was dead at least the Ministry couldn't use her against him.

"Harry, we need to hide, I smell danger." Damien whispered to him.

"Yea, sure." Harry said in his monotonous tone.

"You know, eventually you need to forget about her."

"Well, I can't." He hissed. "Let's just hide and wait for the danger to pass."

Harry silently made his way up a tree where he stretched his legs on a branch, well hidden by leaves and snow. Then his senses were overcome by the most delectable scent he had ever experienced. He breathed deeply to get as much of the scent as he could.

"Found you, Vampire." A feminine voice whispered in his ear.

His stomach blasted outward and he shot off the tree. His blood spurt on the white ground.

"You should have known you couldn't hide. The two of you are quite easy to track and you guys stink." The girl jumped down and landed next to him. "I stand corrected, you are actually quite pleasant. Unfortunately," She pointed her second flintlock pistol to his head. "I have a mission to complete."

She was about to pull the trigger when Damien tackled her to the ground.

"I told you I would keep him alive. I will not let you kill him just because you're a mutt now." Damien growled.

"Hermione?" Harry groaned as he struggled to sit up.

"Yes Harry, this is the girl who left you." He ripped the cowl off of her face. "The Ministry turned her into a mutt to hunt you. This is not Hermione Granger anymore."

"Hermione, why are you hunting me?"

Damien was about to answer when Hermione cut him off. "I can answer for myself, thank you. I am hunting you because of all the crimes you committed; breaking and entering into Gringotts bank, destroying historical property, 2 charges for that and finally, the murder of several Aurors during your latest escapades."

Harry stared wide-eyed at Hermione.

"You were there with me when I did all of those! You know that I did all those to save the Wizarding World and if the Ministry weren't hunting me, then I wouldn't be running for my life!" He yelled.

"This argument doesn't matter Harry, she won't listen. The Ministry has programed her simply to hunt you, nothing else." Damien said quietly.

"Do you not even remember me Hermione? Did you forget everything we've been through together?" Harry asked.

Suddenly, a small lead ball swung from a tree and smacked Damien off of Hermione, a loud crack indicating broken bones.

"Damn you, Seer." Damien grunted.

"Accio Rapier." Damien's sword flew from his holster to Hermione's hand. "You can either fight me like a man, or run with your tail between your legs. Your choice, either way I'll kill you."

"I won't fight you Hermione. I sill love you and refuse to harm you in any way." He took one small step back and was suddenly lifted upwards by his ankle, hanging on a rope connected to a tree limb. He looked into her amber eyes, with no sign of them ever being he soft brown.

"I know all your moves, as your little leader said, I am part Seer. Everything you do, I have a counter for it. These traps were planted a month ago, I also know that Damien here is trying to reach for his dagger, finds it to dull to be useful, then reaches for his gun, jammed." Damien had done all of those things and Hermione hadn't even looked at him. "And look where you are sweetie, hanging from the same tree I found you in." She quickly tied him with magical ropes.

"You defiantly are the Brightest Witch of the age." Harry muttered under his breath.

"Mr. Nightingale, will you be joining us on our trip to the Ministry? Or do you choose death?"

"I won't leave Harry alone like you." Damien growled.

"Suit yourself. I just thought you wanted to die in your home, but whatever." She grabbed the restrained Vampire and took Harry's hand, then apparted to the Ministry.

The three of them popped into center of the Ministry, the whole staffed waiting for when their huntress said she'd return with the target.

"Got him, brought his friend to. Just as promised." Hermione said as she dragged the two down the hallway.

The Minister walked out of the crowd and began talking to Hermione.

"Well well, I am impressed Ms. Kage, very impressed. You have been gone what, 3 days? And you brought the target in that little time while trained Aurors couldn't bring in in 14 months." The Minister beamed.

"Yes, I know. Technically, it took 5 days, but what can you expect from a Time Lady? The plan is the same, correct, Minister?" She asked.

"Yes Ms. Kage, we will still be following the preset plan."

Out of nowhere, a blue box spun from the ceiling before landing in front of 'Hermione', The door a small door opened on the side and a man with brown hair and a bow tie stepped out.

"Oh Hermione, I'm back!"


	2. Chapter 2

Everyone stared at the man, flabbergasted. All except Hermione.

"Hello, Father." Hermione said coldly.  
The man's face fell.

"Is that it? No squeals or one of your death hugs?"

"Ms. Kage, do you know this man?" The Minister asked.

"The living Last Time Lord born on Gallifrey. My father. The man who abandoned me when I was born."

"What are you talking about Hermione? I never abandoned you, I gave to a safe, caring home and visited you constantly. ."

The Minister began to panic. This man could break the hold he had on his perfect hunter!

"Ms. Kage, that man is your new target."

Suddenly, a brown haired man poked his head out of the door.

"Find Hermione yet, Doctor?"

"Rory, where is Amy?" The Doctor asked quietly.

"Finding her present, why?" Rory asked.

"Keep her inside the TARDIS."

Rory nodded, confused, before going back into the TARDIS.

"Permission to Exterminate on sight, Minister?" Hermione smirked as she watched the Doctor cringe.

"Permission granted , Ms. Kage."

Faster than light, Hermione had pulled out her pistol and pointed it at the Doctor.

"Hermione, please recognize me. I love you darling, remember who I am." The Doctor pleaded.

"You know, I have no idea why you two keep calling me this 'Hermione' person. My name is Alexis Kage, at least thats what I chose as my name. Sorry Mr. Potter, I'm not your precious Hermione girl."

"Potter, you mentioned him before. He's the man you love, what the hell are they making you do?"

"Doctor, she won't listen, trust me I've tried. They've had her and have been playing with her mind for a year now. She doesn't remember any of us.."

The Doctor pulled out the Sonic Screwdriver and scanned 'Alexis'.

"Time Lady, that's normal. You are Hermione- what the hell? Vampire, Seer and Banshee? Where did all those come from?"

'Alexis' was tired of talking. She pulled the trigger and shot his shoulder. She began to walk towards him with her dagger, when Damien, his internal injuries healed, tackled her to the ground.

"Doctor, take Harry with you. He's a very useful person and doesn't have much to return to without Hermione. He can help you get her back."

"Right, well, it seems I'll be changing faces soon. Give me a minute." The Doctors head and arms burst into beams of light. A sort of golden dust was floating around him . When it all settled, he looked completely different.

Hermione began to flail rapidly under Damien.

"No iron ball to save you now eh, Mutt?" He growled.

"This wasn't the plan!" She screamed.

"Let me tell you something about time 'Alexis', at the moment, 3 people can alter it. Two of them are in this room, therefore almost any plans you see with me are bound to change." The Doctor hissed.

"No! I must kill my targets, it has been my goal since I knew who you were!" Hermione yelled, her Banshee emerging slightly.

"I promise to return Hermione, I will free you." Harry said softly.

The Doctor only nodded before he stepped into the TARDIS. "You coming Harry?" He asked.

Harry silently went into the TARDIS. Hermione let out another piercing shriek before the door shut and the TARDIS flashed out of the Ministry.

The Doctor stumbled to the control panel before shrinking into the smallest ball he could form. In the first time a long time, The Doctor began to openly weep.

A red haired woman ran to the Doctor and took him into her arms.

"What the hell happened down there Doctor?" She asked.

"They mutated her, Amy! The twisted h-her mind to hunt me!" He sobbed into Amy's shoulder. "She doesn't even remember me..."

"How could she forget you, her father?" She asked.

"They probably Obliviated her and used the Imperious curse to rewrite her memories." Harry said quietly.

"Who are you? And what did you just say?" The girl named Amy asked.

"Harry Potter, ma'am, I'm a close friend of Hermione or at least, was. And those were spells; Obliviation is a memory eraser while the Imperious Curse is a form mind control." He explained.

"So, you're saying that any memories of me have been permanently erased?" The Doctor asked, hopeless.

"Well, if they obliviated her, then, unfortunately yes. However, if they used an Imperious Curse, they could have just created a split personality." Harry said sadly.

The Doctor slowly rose, remembering that the were still in the presence of a skilled hunter, and started the TARDIS. With only one place on his mind, he left the Ministry.

"Doctor, where are we going?" Rory asked.

"To Stormcage." He said, determined.

The TARDIS hummed and whirred as it began to transport. Then, in an instant, all noises stopped and the Doctor hastily left the TARDIS. He fast-walked until he found the cell he was looking for.

"We'll, aren't you familiar."

"How did you do it?" He demanded.

"Do what sweetie? Have you been...have you been crying?" Dr. River Song asked.

"How the hell did you break the Silence's brainwashing? Why did you stop hunting me?"

"Why are you asking these questions? And you still need to answer me. Have. You. Been. Crying?"

"Yes! And I have a damn good reason for it!" The Doctor screamed.

"And what would that be?"

He gave her a simple name. "Hermione."

River gasped softly. "No...not her. What the hell did they do to my darling daughter?"

"That stupid Ministry of hers has taken away any memories of me, most likely you too, and made her hunt down and kill that Harry Potter boy she fancies. I went there, Harry was tied up and bleeding out of his stomach, then some bloke in a pointy hat told her to kill me. I thought it ridiculous for a second before...before she turned and shot me in the shoulder." The Doctor look ready to sob again.

"W-What are we going to do? What if she knows how to-"

"-use my Vortex Manipulator? Yes mummy dearest, I do remember how I trained myself with my own Vortex Manipulator. In case you didn't notice, I'm quite bright. It's not that hard to punch in a code."

"Hermione...sweetheart what have they done to you?" River said, her eyes blurry.

"Nothing. They took me in and trained me to be a hunter. A perfect hunter. So, my main objective was to exterminate anyone that could be a threat to the Ministry, in other words, a Resistance. And it all starts with Harry James Potter. But then, you showed up, Doctor. You became my target, and please, stop calling me Hermione! That is not my name, my name is Alexis. Alexis Kage."

"That's not your name. Your father left you with the Grangers." River stated.

"Emma and Daniel Granger. Race: Human/ Mughle. Status: Deceased. Cause of Death: Poisoned by Alexis Kage. Good family they were, not sure the Minister wanted them dead." She said, her eyes unfocused as she spoke monotonous.

"You k-killed them?" River stuttered.

"We don't have time for chats with her, River. She inherited your skill with guns and improved it ten-fold." The Doctor unlocked the cell with his Sonic Screwdriver. "If she really wanted to, she would've killed us by now."

"To true, Doctor. But I can't let you leave." Alexis pointed her gun at them, but the Doctor was faster at jamming her gun with the Sonic, breaking some of the internal parts. "You didn't look ahead, did you? For someone who's my daughter, you're pretty bad at manipulating time. Get to the TARDIS River." The two ran quickly to the blue box as Alexis shot but missed. "And you miss a lot."

The door to the TARDIS shut as it began to disappear.

"Sweetie, why are you him again?" River asked, trying to make small talk.

"What do you mean again?" The Doctor found a small mirror and was surprised to find his last regeneration. "What!" He shrieked, his voice reaching a new octave. "Why am I this? How the hell did this happen?" He made a series of uncomprehensive noises. "What?"


End file.
